RotRL as it is now is still a 3.5 AP, so are the next 2 or 3. That isn't really a huge problem but since PF characters are a bit stronger than 3.5 you'll have to adjust the encounters sometimes to compensate.

As Dabbler said there's a new edition of RotRL in the making that updates it to PF rules.

Of the ones I own or play, Jade Regent is the one I like the least.
Carrion Crown is my favorite so far, but Skulls and Shackles might take first place. Next was Curse of the Crimson Throne, which we liked a lot.

DM'ing CotCT was not so hard to DM even if it was 3.5. Tome of Horrors Complete for PFRPG came out while I dm'd part four of that series and there are quit a few monsters that came out of that series.

As for RotRL, I can hardly wait for the hardcover coming out this summer. Have heard many good things but have never read/seen it.

Wow, it sounds like almost all the big APs are really good! Good to hear, as I have not run in any of them, except a little bit in RotRL and CotCT (did not finish them) and am currently running in Council of Thieves. I read it's not that great, though I'm having fun so far, and I really like the whole Cheliax/Hellknights/devils setting.

I heard this question asked before, and one common answer was the Legacy of Fire. How does that rate compared to CotCT, RotRL?

Runelords will be the most Newb-friendly, I think, once the rerelease drops. They got a chance to iron out the exceptionally deadly encounters. ("X")

I like Legacy of Fire a lot, personally, but it would need to be updated to PF. Conversion isn't terribly hard or mandatory, but for beginners it is nice to have everything laid out correctly.

Kingmaker could definitely be a contender, just because the sandbox format means less can go wrong with the meta-plot. Serpent's Skull has a stronger plot but still seems very straight-forward by comparison to others.

...am currently running in Council of Thieves. I read it's not that great, though I'm having fun so far, and I really like the whole Cheliax/Hellknights/devils setting.

Different strokes and all, you know. Sarah and I were in Italy at the Lucca Games and Comics convention last fall and the Italians were FLIPPING OUT over this AP. Like every question I fielded was about it, and it wasn't even the newest one released in the language. Weird that Italy would have a thing for schemes, politics, and Hell, right? :P

Legacy of Fire is my favorite, it's setting was beautifully written and it very epic in its scope. But Skull and Shackles might just supplant it as my favorite, cuz well pirates, treasure hunts, ships just too much awesome.

I've run the first half of Rise of the Runelords, and my players all loved it. It reads very well. I'll second votes for waiting on the re-release for ease of play, though, if you're new to running Pathfinder.

I read bits and pieces of Curse of the Crimson Throne, and while my memory is hazy on a lot of it, it has some great elements. Book 5, in particular (Skeletons of Scarwall), looks like it would be a blast to run.

I read all of Kingmaker and I like it in principle, but in execution its scope is VERY wide. It does have a lot of nice rules subsystems, though, including nation building and streamlined mass combat - and we have had a LOT of fun with the latter!

But my heart is still with Carrion Crown for the ultimate win. I'd argue that it's actually pretty newbie-friendly if you take things at face value and don't overthink the stat blocks for unique monsters (especially in book 1 - there's some wonkiness there mechanically, but the results are stunning). The main trip-up for a new GM in Carrion Crown will be some of the optional subsystems, especially the brutal Trust mechanic in Haunting of Harrowstone (there's several threads devoted to making this feature work right here on the boards). There's also a pretty large number of NPCs to run across the entire AP, so work on your funny voices before you begin playing!

But if you like horror-themed adventures and creature-feature encounters, CC is the way to go. The underlying story presented in the AP is astonishingly well-plotted, provided you read ahead and telegraph the archvillain well in advance of his first true appearance in the AP. There's also a lot of room for homebrew expansion both along the way and after the finale, especially if you pick up Dungeons of Golarion and read up on Gallowspire. We're about to wrap up Trial of the Beast next week, and I'm itching to get started on Broken Moon soon thereafter!

Another vote for Runelords. No extra mechanics to worry about (like kingdom building or ships), just straight-forward site-based adventures.

Also, although I've never actually played through it, it's probably the AP I've spent the most time reading because it is the most interesting. It has a certain rough-and-tumble charm that was eventually lost as the products became glossier.

My advice though is to go for one you like the look of. Be aware that Kingmaker, Serpent's Skull and Second Darkness need extra work from a GM either because of their nature or because they need some remedial work.

Age of Worms and Savage Tide are in a statistical dead heat, as far as I'm concerned.

I've been re-reading Savage Tide and thoroughly loving it. But again, it's from 3.5. Not a good newbie choice, IMO. I don't know that I would attempt to run it in its entirety, but I might co-opt the second half as a wrap-up for a high level campaign I'll be running in the future.